GenBank Batch Download

Question

[virpatel3]

I have a list of bacteriophage names. A program that I am using would like the GenBank entries for all of these phage.

For instance: http://www.ncbi.nlm.nih.gov/nuccore/339754473

Now, there is the option to download all of these by hand using the Send feature. But is there a second, faster way to do so? I found the Entrez utilities feature, but I'm not sure if that's what I'm looking for. Does anyone have any suggestions?

Answer 1

[5heikki]

Parse the accessions from this table and fetch them with entrez direct, e.g.

efetch -db nuccore -id NC_015250 -format gb > NC_015250.gbk

Alternatively something like:

esearch -db genome -query "Acinetobacter phage 133" | elink -target nuccore | efetch -format gb > thisGenome.gbk

Answer 2

[BioApps]

Hi

I am building a program that is doing this. Full graphic interface. It will be part of a larger project called NCBI Blaster.

NCBI BLAST DB Downloader and NextGen Workbench will also be integrated into NCBI Blaster.

I will post these day a beta (but functional version).